Submitted by Edineia Teixeira (edineia.teixeira@unioeste.br) on 2018-04-13T14:51:51Z No. of bitstreams: 2 Carola_Gutfreund2017.pdf: 2632451 bytes, checksum: 73a0a3864936cf1f3347866fcda5f49f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-04-13T14:51:51Z (GMT). No. of bitstreams: 2 Carola_Gutfreund2017.pdf: 2632451 bytes, checksum: 73a0a3864936cf1f3347866fcda5f49f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-04-18 / Large hydroelectric dams along the Paraná River have caused severe impacts on fish communities as they represent obstacles to long-range migratory species that need to migrate to complete their life cycle. Dams can bring numerous problems through the interception of migratory routes and reduction of spawning areas. The most common measures used to mitigate the effect of these physical obstacles is the implementation of fish ladders. It is not only important to implement these structures, but also to monitor them. This study was performed at the Engenheiro Sergio Motta Hydroelectric Power plant in the Upper Paraná River during December/2012 and March/2016. The aim of it was to evaluate the effectiveness of this structure in relation to the attractiveness rate and passage efficiency of to two Neotropical fish species in the fish ladder. In total, 563 fish of genus Leporinus (447 Leporinus obtusidens and 116 Leoporinus piavussu) were tagged and released with the implementation of 32-mm programmable transponders (PIT-tags). Radio Frequency Identification (RFID) was used to monitor the system. The attractiveness of the ladder was 8.7%. The minimum time to find it was 1.49 days for the fish released upstream and the maximum time was 449.86 days for the individuals released downstream. The release site had a significant influence on the entry rate of fish released on the other side of the river. No detection was observed for fish released downstream and upstream on the right bank of the river. Only the fish released on the same site where the fish ladder is located were detected, suggesting low attractiveness of the ladder in relation to the studied species. In the course of this study it was verified that for the two species studied it would be extremely important to increase the attractiveness at the entrance of the ladder, as well as to build a second ladder for fish on the right side of the river. / As grandes hidrelétricas ao longo do Rio Paraná têm causado impactos severos nas comunidades de peixes, pois representam obstáculos para as espécies migradoras de longa distância, que precisam migrar para completar seu ciclo de vida. As barragens podem trazer inúmeros problemas por meio da intercepção das rotas migratórias e redução das áreas de desova. As medidas mais comuns utilizadas para mitigar o efeito desses obstáculos físicos é a implementação de escadas para peixes. Não é somente importante a implementação dessas estruturas, como também o monitoramento. Esse estudo realizado na escada para peixes da Usina Hidrelétrica Engenheiro Sérgio Motta no alto Rio Paraná no período de dezembro/2012 a março/2016 teve como objetivo avaliar a efetividade dessa estrutura em relação a taxa de atratividade e eficiência de passagem para duas espécies de peixes migradores neotropicais. No total, foram marcados e liberados 563 peixes do gênero Leporinus (447 Leporinus obtusidens e 116 Leoporinus piavussu) com a implantação de transponders com códigos programáveis (PIT-tags) de 32 mm. Foi utilizado o sistema de rádio frequência (RFID Radio Frequency Identification) para o monitoramento do sistema. A atratividade da escada foi de 8,7%. O tempo mínimo para encontrar a escada correspondeu a 1,49 dias para os peixes liberados a montante e o tempo máximo foi de 449,86 dias para os indivíduos liberados a jusante. O local de liberação influenciou significativamente a taxa de entrada dos peixes liberados na margem oposta do rio, sendo que nenhuma detecção foi observada para peixes liberados na margem direita, tanto a jusante como a montante. Foram detectados apenas os peixes liberados na mesma margem onde a escada para peixes está localizada, sugerindo baixa atratividade da escada para as espécies analisadas. No decorrer deste estudo verificou-se que para as duas espécies estudadas seria extremamente importante aumentar a atratividade na entrada da escada, como também a construção de uma segunda escada para peixes no lado direito do rio.

The use of pop-up satellite archival tags (PSATs) eliminates many of the limitations associated with acoustic and conventional tags by using fishery-independent data collection and retrieval. Previous research techniques have provided information on longer-term movements, migrations, and behavior patterns, but there is still a need for additional tagging studies using tags with depth and light data and increased memory that will further define the short-duration activity patterns and habitat utilization of juvenile swordfish in the western North Atlantic. PSATs have been successfully used on other large pelagic fishes, but have yet to be used on juvenile swordfish. This study investigated two main topics: a) the post-release survival rates of juvenile swordfish after being released from the recreational rod-and-reel fishery and commercial swordfish buoy gear fishery in the Florida Straits, and b) the habitat utilization of juvenile swordfish following release. High-resolution PSAT technology was used to estimate the post-release survival of 16 individual juvenile swordfish captured with standard recreational or buoy fishing gear and techniques in the southeast Florida swordfish fishery. Analysis of release mortality estimates was done using the “Release Mortality” Program. Five of the fourteen reporting tags showed a mortality within 48 hours, for a release mortality rate of 35.7%. However, no common thread could be found among the five mortalities. Results of the Release Mortality program indicated that if the true mortality rate was 35.7%, approximately 1800 tags would have to be deployed to increase the precision of the mortality estimates to +/- 5% of the true value. The nine surviving fish varied in straight-line distance traveled and in direction, and could withstand a wide range of temperatures. A deterministic, periodic model was developed to fit to the data and describe the fishes’ habitat utilization. This model identified both diurnal and lunar signals in the data, confirming that juveniles do move vertically based on the daily cycle of the sun and the lunar cycle of the moon and that their diurnal movements are much greater than their lunar movements. The results of this study can be valuable to management practices in future stock assessments and decisions regarding mandatory release of undersized fish.

Philosophiae Doctor - PhD / This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent. / South Africa

The master thesis is focused on professional and user-generated metadata with emphasis on content metadata. It describes metadata in general, their important characteristics, functions, and types, and defines other related terms. The professional content metadata and user-generated metadata are described in more detail. The analytical part aims to compare professional and user-generated content metadata. For this purpose, a dataset of metadata statements on fiction books collected from dozens of databases was used. It also aims to determine whether user-generated metadata bring additional information to metadata created by professionals.

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第21886号 / エネ博第387号 / 新制||エネ||75(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 森井 孝, 教授 木下 正弘, 教授 片平 正人 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DGAM

Oligosaccharides play very crucial biological roles in the human body. They are structurally diverse and very challenging to analyze. In an attempt to contribute towards the analysis of oligosaccharides in the growing filed of 'Glycomics', we explored different ways to make novel efficient oligosaccharide tags to label N -linked oligosaccharides from glycoproteins. We synthesized and characterized various oligosaccharide tags which are useful to analyze the oligosaccharide by mass spectrometry, HPLC, and bioaffinity. In these tags we incorporated ar UV/fluorescent core, a biotin moiety and an amino/azido/alkyne terminus. We varied the structures of the tags for improved solubility in common organic solvents. These tags were used to label standard oligosaccharides, and the labeling efficiency was evaluated.

As urban areas expand, agricultural lands become increasingly important habitat for many species. Compared to some types of agricultural land-use, ranchlands provide vast expanses of minimally modified habitat that support many threatened and endangered species. Conservation biologists can promote ecologically sound management approaches by quantifying the effects of agricultural practices on resident species. I examined the effects of pasture management, cattle grazing, and landscape characteristics on both adult and larval treefrogs in a ranchland in south-central Florida. I experimentally determined optimal deployment of artificial treefrog shelters constructed of polyvinylchloride (PVC) pipe to efficiently sample adult treefrogs (Chapter 1). Seventy-two shelters were hung on oak trees (Quercus virginiana) and cabbage palm trees (Sabal palmetto) with smooth trunks or boots (residual palm fronds), at all possible combinations of three heights (2, 3, and 4 m), four compass directions (N, S, E, and W) and two water levels (with or without 10 cm). Shelter residence was completely dominated by the Squirrel Treefrog, Hyla squirella (N = 65). Significantly fewer H. squirella were found in shelters on palms with boots than on smooth palms or oak trees (0.29 ± 0.21 [mean ± 1 SE hereinafter] versus 1.3 ± 0.21 and 1.1 ± 0.21, respectively), and shelters with water had slightly more H. squirella than those without (1.5 ± 0.19 versus 0.88 ± 0.19, respectively). Orientation and height did not affect the number of treefrogs encountered; thus, the optimal protocol is to deploy shelters on either smooth palms or oak trees, with water, at 2 m height for easy sampling, and in random compass orientations. I used this protocol to sample H. squirella in woodlots surrounding twelve wetlands and examined how time, frog stage and sex, and landscape features influenced treefrog survival, recapture and site fidelity (Chapter 2). I deployed 15 shelters/ha of woodlot within a 100 m buffer around each wetland. I sampled shelters three times during the fall breeding season, removed all shelters to force frogs to overwinter in natural refugia, and replaced shelters for the final spring sampling. During sampling periods, I sexed, measured, and individually marked each frog using visual implant elastomer (VIE) tags. I used Program MARK to build linear models that included either gender group (female, male or juvenile) or life history stage (adult, juvenile) and either time (sampling interval 1, 2, or 3) or season (fall, spring). I used the most informative model as a null model to assess effects of landscape covariates on survival and recapture. Females had higher survival than either males or juveniles, for which estimates were similar (0.867 vs 0.741 and 0.783, respectively). Survival did not vary over time, although there was some support for an effect of season, with lower survival during the final over-wintering period than in the fall intervals (relative variable importance: group = 0.730; stage = 0.134; time = 0.200; season = 0.310). Adults had higher recapture rates than juveniles (average recapture 0.214 vs 0.102), and recapture for both stages varied over time, with highest recapture in sampling interval two (relative variable importance: group = 0.262; stage = 0.514; time = 0.513; season = 0.229). Hyla squirella was extremely site loyal; no individuals moved between sampling sites, and 95% of recaptured individuals were in their original shelter. Strong terrestrial site fidelity calls into question the traditional "ponds as patches" metapopulation view of treefrog population dynamics. Area of woodlot within 250 m was the most important landscape variable in explaining additional variation in both survival and recapture. Frogs had higher survival and lower recapture in larger woodlots, indicating that intact, contiguous woodlots are higher quality habitat than more fragmented woodlots. Neither survival nor recapture varied with wetland grazing treatments or between pasture types. Finally, I experimentally assessed the effects of cattle grazing and pasture management on larval H. squirella. I selected four wetlands: two in semi-natural pastures (SN) and two in intensively managed pastures (IM). One wetland in each pasture type was fenced so that it was released from cattle grazing (R). I collected three clutches of H. squirella eggs (Clutches A, B, and C) and reared tadpoles in the laboratory until Gosner stage 25. In each wetland, I deployed a total of 50 tadpoles from each clutch into 105 L pens constructed of plastic laundry baskets and mesh window screening. Clutch significantly affected tadpole survival, with Clutch A having the highest percent survival, followed by Clutch B and finally Clutch C (41.66, 32.11 - 53.95 [mean, 95% confidence limits hereinafter]; 9.00, 6.76 - 11.88; 2.89, 2.02 - 4.01, respectively). Wetland type also affected survival, with SN wetlands supporting significantly higher survival than IM wetlands (SN-R: 53.95, 32.88 - 88.13; SN-G: 18.95, 11.30 - 31.36 vs IM-R: 7.32, 4.13 - 12.49; IM-G: 1.09, 0.29 - 2.39). Genetic variation in survival confirms the potential for H. squirella to adapt to rangeland management, but extremely low survival of some clutches indicates that few clutches may be able to survive in low quality wetlands, such as IM-G wetlands. Higher survival in SN pasture wetlands suggest this is a superior habitat and future management objectives should conserve semi-natural pastures and limit further modification of intensively managed pastures, including removing woodlots near wetlands.

Avec l'explosion de l'Internet des Objets (IoT), de nouveaux dispositifs permettant de tagguer les objets sont nécessaires afin de permettre non seulement leur identification mais aussi d'assurer des communications fiables et de nouvelles fonctionnalités comme la détection, la localisation ou la capture d'informations. Cette tendance s'appuie sur la technologie bien établie qu'est la radiofréquence par identification (RFID) et donc l'utilisation d'étiquettes (ou tags) faibles coûts et télé-alimentés. Dans ce contexte, de nombreux travaux au niveau de la couche d'application se tournent vers la mise au point de traitements logiciels complémentaires visant à produire de nouveaux types d'information. D'autres travaux visent à améliorer la couche physique avec l'objectif de miniaturiser encore le tag mais aussi de le doter de nouvelles capacités. Jusqu'à présent, il n'existe quasiment pas de travaux concernant la transmission du signal et aucun sur l'exploitation du comportement non-linéaire des puces RFID. Cette thèse vise à étudier les phénomènes non-linéaires produits lors d'une communication RFID.Dans la première partie, deux plateformes de mesure et de caractérisation spécifiques ont été développées : la première vise à observer les signaux au cours d'une communication RFID, et alors caractériser et analyser les effets liés aux phénomènes non linéaires ; la seconde permet d'effectuer différentes mesures directement sur les puces et les caractériser en termes d'impédance, production d'harmoniques et sensibilité. Ces plateformes ont permis : 1) de mettre en évidence que les fréquences harmoniques sont porteuses d'informations qui peuvent être exploitées et même offrir de nouvelles fonctionnalités ; 2) d'obtenir de nombreuses informations sur les propriétés des puces et d'en établir un modèle électrique précis ; 3) de déterminer des critères permettant d'évaluer la performance des tags dans le contexte étudié.Dans la deuxième partie, plusieurs nouveaux tags RFID ont été conçus, fabriqués, mesurés et évalués. Ces nouveaux tags fonctionnent non seulement dans la bande UHF mais aussi sont adaptés à la troisième harmonique dans la bande des microondes. Une méthodologie et des lignes directives d'aide à la conception de ce type de tags ont été établies et s'appuient sur les deux plateformes développées afin de caractériser les différents éléments. Dans un même temps, les effets liés à la fabrication ont aussi été étudiés et des études paramétriques ont permis de mettre en évidence l'effet sur les performances de la géométrie de l'antenne et du type de puce utilisée.Dans une troisième partie, les études se sont focalisées à exploiter les effets non-linéaires des dispositifs de redressement. L'idée générale est de coupler la RFID passive avec les dispositifs de transferts de puissance et de récupération d'énergie avec pour objectifs 1) de maximiser l'efficacité de conversion RF – continu 2) et d'augmenter la distance de lecture des tags passifs. Plusieurs prototypes ont été réalisés et leurs performances ont été démontrées.L'ensemble de ces travaux a mis en évidence un nouveau concept de communication RFID exploitant les non-linéarités générées par les puces RFID. Ce concept ouvre la voie à de nouvelles applications. et a fait l'objet d'une demande de brevet international. / Powered by the exploding popularity of the Internet-of-Things (IoT), the demand for tagged devices with labels capable to ensure a reliable communication with added functions beyond the identification, such as sensing, location, health-care, among others, is growing rapidly. Certainly this growing is headed by the well-established Radio Frequency Identification (RFID) technology, and the use of wireless low-cost self-powered tags, in other words passive RFID tags, is the most widespread used alternative. In the constant evolution on this field, usually new software treatments are offered at the application layer with the objective to processing data to produce some new information. Further works aimed at improving the physical layer around the tag antenna miniaturization and matching techniques. So far, little or no work had been done on the exploitation of the communication channel, and certainly none has been done on the exploitation of the non-linear behavior of RFID chips.After presenting the RFID technology and phenomena produced by Radio Frequency (RF) non-linear devices, and leaning in some nearby works on the field, the core of this thesis starts by exposing two characterization platforms for the evaluation of non-linear phenomena presented during the reader-tag communication. One is specialized in radiating measurements considering the whole tag (antenna and chip) under test. The other is specialized in conducted measurements directly over RFID chips, allowing performing different parametric studies (power dependency, impedance, harmonic production, sensitivity). The characterization results show that harmonic signals generated from the passive RFID chip carry information.By exploiting the characterization results and to verify the hypothesis of exploitation of non-linearities in RFID, i.e. the use of harmonic signals, the research is pursued by designing, fabricating, and measuring four different configurations of RFID tags. The new RFID tags operate at the fundamental frequency in the UHF band and at its $3^{rd}$ harmonic in the microwave band. Antenna design policies, fabrication details, and parametric studies on the performance of the new prototypes are presented. The parametric study takes special care in the antenna structure, kind of chip used, received power, and read range.Finally, some alternatives approaches for the exploitation of non-linear effects generated by rectifying devices are presented. Some theoretical aspects and experimental results are discussed linking the passive RFID technology to the theories of Wireless Power Transfer (WPT) and Electromagnetic Energy Harvesting (EEH). The solution takes advantage of the non-linear nature of rectifying elements in order to maximize the RF-to-DC conversion efficiency of EEH devices and increase the read range of passive RFID tags. The solution triggers on the design of a RF multi-device system. The design procedure and tests consider three non-linear phenomena: (1) the impedance power dependency, (2) the harmonic production, and (3) the rectifying dependence on the RF waveform.

<p>The two techniques aqueoustwo-phase partitioning and expanded bed adsorption that bothare suitable for primary protein recovery were studied. Most ofthe work was focused on partition in aqueous two-phase systemsand in particular on the possibility to effect the partitionbehaviour by fusion of short peptide tags or protein domains tothe target protein.</p><p>The partitioning of fusionproteins between different variants of the domain tag Z and thenaturally occurring protein DNA Klenow polymerase were studiedin Breox/Reppal aqueous two-phase systems. Most studies wereperformed with cell homogenate. The Breox/Reppal system was infocus because if the fusion protein can be partitioned to theBreox-rich top phase the next step can be a thermoseparatingaqueous two-phase system. When the Breox phase is heated to50°C it switches from a one-phase system to a two-phasesystem resulting in an almost pure water rich top phase andhighly concentrated Breox-rich bottom phase. The Breox can thenbe reused and the protein recovered from the water phase. TheZ-domain was genetically modified in different ways to Z_basic1, Z_acid2and Z_trp12and fused to the Klenow protein to try toenhance partitioning to the Breox-rich phase. From theexperiments it was not possible to observe any effects on thepartition behaviour irrespectively of tested properties of thedomain tag. Despite the absence of domain tag effects highK-values, i.e. partition to the Breox-rich top phase, wereobserved in the Breox/Reppal system. However, the proteinK-values seemed to be rather sensitive to the cell homogenateload and showed a tendency to decrease with increased cellhomogenate load. Also increased phosphate concentration reducedthe K-values. The partitioning of cell debris also seemed todependent on the cell homogenate load. At higher homogenateload (<=20g DW/L) clear Breox-rich top phases were observedwith the cell debris collected in Reppal-rich bottomphases.</p><p>Two different tetrapeptides,AlaTrpTrpPro and AlaIleIlePro were inserted near the C-terminusof the protein ZZT0. The Trp-rich peptide unit stronglyincreased both the partitioning of ZZT0 into the poly(ethyleneglycol) (PEG)-rich phase in a PEG/potassium phosphate aqueoustwo-phase system and its retention on PEG and propylhydrophobic interaction chromatographic columns with potassiumphosphate as eluent in isocratic systems. Both the partitioningand the retention increased with increasing number of Trp-richpeptide units inserted into ZZT0. Insertion of Ile-richtetrapeptide units affected the partitioning and retention to amuch lesser extent. Partition and modelling data also indicateda folding of inserted Trp and Ile tetrapeptide units, probablyto minimise their water contact. It was also investigated howto predict the partitioning of proteins in isoelectricPEG/phosphate aqueous two-phase systems.</p><p>The capture ofß-galactosidase from<i>E. coli</i>cell homogentate (50g DW/L) by metal chelatexpanded bed adsorption was studied. These experiments showedthat capture, with a certain degree of selectivity, andclarification of ß-galactosidase could be achieved from acell homogenate. However, a rather low recovery of about 35 %was obtained at a capacity of 0.25mg/mL of gel. Thus, severalparameters remain to be optimised like the load buffercomposition and the cell homogenate load.</p><p><b>Keywords:</b><i>E. coli</i>, aqueous two-phase systems, fusion proteins,hydrophobic interaction chromatography, expanded bedadsorption, ß-galactosidase, Klenow polymerase, Z-domain,peptide tags</p>

A coccidiose aviária é uma doença entérica causada por protozoários parasitas do gênero Eimeria. Visando uma maior compreensão dos mecanismos moleculares envolvidos na regulação do ciclo de vida dos parasitas, foram geradas 15.000 seqüências expressas (ORESTES) para cada uma das três espécies mais importantes: E. tenella, E. maxima e E. acervulina. O presente trabalho consistiu no desenvolvimento de componentes de anotação automática de seqüências para o sistema EGene, plataforma previamente desenvolvida pelo nosso grupo (Durham et al. Bioinformatics 21: 2812-2813, 2005) para a construção de processamentos encadeados (pipelines). Estes componentes foram utilizados para a construção de pipelines de anotação automática de seqüências-consenso obtidas a partir da montagem dos ORESTES de Eimeria spp. A anotação consistiu na identificação dos genes e atribuição da função dos respectivos produtos protéicos, baseando-se em um conjunto de evidências. As seqüências também foram classificadas e quantificadas utilizando-se um vocabulário controlado de termos de ontologia gênica (GO). / Avian coccidiosis is an enteric disease caused by protozoan parasites of the genus Eimeria. Aiming at obtaining a better understanding of the molecular mechanisms that regulate the life cycle of the parasites, our group generated 15,000 expressed sequences (ORESTES) for each one of the three most important species: E. tenella, E. maxima and E. acervulina. In the present work, we report the development of a set of components for the automated sequence annotation through EGene, a platform for pipeline construction previously described by our group (Durham et al. Bioinformatics 21: 2812-2813, 2005). These components were used to construct pipelines for the automated annotation of assembled sequences of ORESTES of Eimeria spp. The annotation process consisted in the identification of genes and the corresponding protein function based on a set of evidences. The sequences were also mapped and quantified using a controlled vocabulary of gene ontology (GO) terms.